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Review
, 98 (2), 195-212

Placement of Attine Ant-Associated Pseudonocardia in a Global Pseudonocardia Phylogeny (Pseudonocardiaceae, Actinomycetales): A Test of Two Symbiont-Association Models

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Review

Placement of Attine Ant-Associated Pseudonocardia in a Global Pseudonocardia Phylogeny (Pseudonocardiaceae, Actinomycetales): A Test of Two Symbiont-Association Models

Ulrich G Mueller et al. Antonie Van Leeuwenhoek.

Abstract

We reconstruct the phylogenetic relationships within the bacterial genus Pseudonocardia to evaluate two models explaining how and why Pseudonocardia bacteria colonize the microbial communities on the integument of fungus-gardening ant species (Attini, Formicidae). The traditional Coevolution-Codivergence model views the integument-colonizing Pseudonocardia as mutualistic microbes that are largely vertically transmitted between ant generations and that supply antibiotics that specifically suppress the garden pathogen Escovopsis. The more recent Acquisition model views Pseudonocardia as part of a larger integumental microbe community that frequently colonizes the ant integument from environmental sources (e.g., soil, plant material). Under this latter model, ant-associated Pseudonocardia may have diverse ecological roles on the ant integument (possibly ranging from pathogenic, to commensal, to mutualistic) and are not necessarily related to Escovopsis suppression. We test distinct predictions of these two models regarding the phylogenetic proximity of ant-associated and environmental Pseudonocardia. We amassed 16S-rRNA gene sequence information for 87 attine-associated and 238 environmental Pseudonocardia, aligned the sequences with the help of RNA secondary structure modeling, and reconstructed phylogenetic relationships using a maximum-likelihood approach. We present 16S-rRNA secondary structure models of representative Pseudonocardia species to improve sequence alignments and identify sequencing errors. Our phylogenetic analyses reveal close affinities and even identical sequence matches between environmental Pseudonocardia and ant-associated Pseudonocardia, as well as nesting of environmental Pseudonocardia in subgroups that were previously thought to be specialized to associate only with attine ants. The great majority of ant-associated Pseudonocardia are closely related to autotrophic Pseudonocardia and are placed in a large subgroup of Pseudonocardia that is known essentially only from cultured isolates (rather than cloned 16S sequences). The preponderance of the known ant-associated Pseudonocardia in this latter clade of culturable lineages may not necessarily reflect abundance of these Pseudonocardia types on the ants, but isolation biases when screening for Pseudonocardia (e.g., preferential isolation of autotrophic Pseudonocardia with minimum-nutrient media). The accumulated phylogenetic patterns and the possibility of isolation biases in previous work further erode support for the traditional Coevolution-Codivergence model and calls for continued revision of our understanding how and why Pseudonocardia colonize the microbial communities on the integument of fungus-gardening ant species.

Figures

Fig. 1
Fig. 1
Phylogeny of Pseudonocardia reconstructed by Mueller et al. (2008) from 16S rRNA gene sequence information. This reconstruction was based on a limited sample of 85 Pseudonocardia sequences available at GenBank in September 2007 and excluded sequence information in regions of unambiguous alignment (i.e., the reconstruction was not based on the 16S secondary-structure modeling employed in the present study). The clade labels on the far right correspond to the labels in Fig. 2a and b of the present study (Clade 1&2 was called “compacta-group” and Clade 3 was called “alni-group” in Mueller et al. 2008). This previous analysis revealed close affinities between many ant-associated (shaded) and environmental Pseudonocardia (unshaded), and predicted that future surveys will discover environmental Pseudonocardia nesting in groups appearing “ant-specific” at that time. This prediction is tested in the phylogenetic reconstruction shown in Fig. 2a and b, which is based on four times the sequence information that has become available for Pseudonocardia since the study by Mueller et al. (2008)
Fig. 2
Fig. 2
Phylogeny of Pseudonocardia reconstructed for 325 taxa under the maximum-likelihood criterion from 16S rRNA gene sequence information. Ant-associated Pseudonocardia are boxed (shaded background); environmental Pseudonocardia are unboxed. Attine-associated lineages are closely related to soil-dwelling or endophytic Pseudonocardia lineages, indicating frequent recruitment of free-living Pseudonocardia into association with ants. Support values are inferred from 100 ML bootstrap pseudoreplicates. Each taxon label gives the method of characterization (sequencing of 16S amplicons from cultured isolates; sequencing of cloned 16S amplicons from environmental surveys; pyrosequencing of 16S amplicons; direct PCR from ants) and the GenBank accession, followed in parentheses by the ant species name from which a bacterium was sampled, the ant collection ID (e.g., UGM010817-01), the source from which the sequence was obtained (worker, garden, soil, plant, etc.), and the collection location. The attine ant genera are abbreviated as: Ac. = Acromyrmex; Ap. = Apterostigma; At. = Atta; Cy. = Cyphomyrmex; My. = Mycocepurus; Tr. = Trachymyrmex
Fig. 2
Fig. 2
Phylogeny of Pseudonocardia reconstructed for 325 taxa under the maximum-likelihood criterion from 16S rRNA gene sequence information. Ant-associated Pseudonocardia are boxed (shaded background); environmental Pseudonocardia are unboxed. Attine-associated lineages are closely related to soil-dwelling or endophytic Pseudonocardia lineages, indicating frequent recruitment of free-living Pseudonocardia into association with ants. Support values are inferred from 100 ML bootstrap pseudoreplicates. Each taxon label gives the method of characterization (sequencing of 16S amplicons from cultured isolates; sequencing of cloned 16S amplicons from environmental surveys; pyrosequencing of 16S amplicons; direct PCR from ants) and the GenBank accession, followed in parentheses by the ant species name from which a bacterium was sampled, the ant collection ID (e.g., UGM010817-01), the source from which the sequence was obtained (worker, garden, soil, plant, etc.), and the collection location. The attine ant genera are abbreviated as: Ac. = Acromyrmex; Ap. = Apterostigma; At. = Atta; Cy. = Cyphomyrmex; My. = Mycocepurus; Tr. = Trachymyrmex
Fig. 3
Fig. 3
16S rRNA secondary structure model for P. carboxydivorans (GenBank accession EF114314; type strain Y8). The Supplemental Information presents additional secondary structure models for four additional species within the genus Pseudonocardia (P. kongjuensis, P. halophobica, P. spinosispora, P. yunnanensis). Canonical base pairs (G:C, A:U) are shown with tick marks, wobble (G:U) base pairs with small closed circles, A:G base pairs with large open circles, and all other non-canonical base pairs with large closed circles 2002). Bacterial 16S rRNA secondary structure diagrams for the modeled Pseudonocardia species are available at the Comparative RNA Web Site http://www.rna.ccbb.utexas.edu/DAT/3C/Structure/index.php, http://www.rna.ccbb.utexas.edu/SIM/4D/TOL/.

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